Inflammation is the foundation for cancer and degenerative/autoimmune diseases. Small changes in diet and exercise, e.g. omega-3 oils, vitamin D, low starch, and maintaining muscle mass, can dramatically alter predisposition to disease and aging, and minimize the negative impact of genetic risks. Based on my experience in biological research, I am trying to explain how the anti-inflammatory diet and lifestyle combat disease. 190 more articles at http://coolinginflammation.blogspot.com

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Monday, January 19, 2015

The year 2014 began with my posts on damage to the gut microbiotacaused by antibiotics, processed foods and excess hygiene.I lamented the inadequacy of information from the media on damage/repair of the gut bacteria and highlighted medical myths with a post on some of Dr. Oz’s own ills that are self-inflicted by his diet and hygiene recommendations.I also started to discuss how to cure autoimmune diseases by repairing damaged gut flora and by avoiding the antibiotic activity present in many common drugs.

With my 200th post in March, I summarized my thoughts on the causes and cures of common diseases in a series of diagrams on:

I illustrated the relationships among diet, inflammation and diseases mediated by gut flora that I have discussed, since I started my blog in 2008. Now after a couple of hundred articles and more than two million visits to my blog, I think that I am starting to grasp some of the major issues that cause inflammatory diseases. The cures also now seem obvious.

Antibiotics Contribute to Autoimmune Diseases

Some species of gut bacteria are needed for the development of the aggressive half of the immune system and other species are needed for the suppressive half. Thus, starving or poisoning gut flora leads to immune system problems and diseases. Antibiotics are a quick way of crippling the immune system. It seems that the aggressive part of the immune system is less fragile, because in most cases antibiotic treatments produce autoimmune disease due to loss of bacteria that are needed for development of immune cells that block the aggressive half of the immune system from attacking innocuous cells of the body or environment, i.e. antibiotics usually trigger deficient tolerance, and autoimmunity.

Feed the Gut Microbiome for a Healthy Immune System

Diet provides food for the body and flora. Protein and fat are the macronutrients needed for the body, while the gut microbiota lives off of plant polysaccharides (except starch) that pass through the small intestines undigested into the colon. The hundreds of plant polysaccharides are hydrolyzed by hundreds of enzymes made by gut flora and produce short chain fatty acids, e.g. acetate and butyrate, that feed colon cells. Food processing systematically removes polysaccharides that feed gut flora and compromises the components of the immune system dependent on those bacteria.

Repairing the Gut Microbiome by Eating the Missing Bacteria

It is easier to see that eating a diet that lacks food for the gut microbiota will be a problem, than it is to figure out where to find replacements for lost species of gut bacteria. The only way that bacteria get into the gut is down the throat. To repair a damaged gut microbiota requires both changing diet and introducing the missing types of bacteria by eating them. Eating dairy probiotics and fermented vegetables can provide a quick, but only temporary fix. Most of the needed bacteria are more common in soil than in food.

Phytochemicals Are First and Foremost Antibiotics

I was shocked that my background in phytochemicals didn’t lead more directly to a major culprit causing modern diseases. The gut microbiota is clearly a major factor in health and sickness. Antibiotics that kill bacteria, damage the gut microbiota. It is also unsurprising that processing food to reduce soluble fiber, damages gut flora, by systematically depriving gut bacteria of their major source of food. The proliferation of antimicrobial products also damages the gut flora. What I missed in this onslaught of modern lifestyles on the gut microbiota, was the major player in antibiotic resistance — phytochemicals are natural antibiotics.

I Missed the Antibiotic Activity of Common Medicines

I studied phytochemicals and wrote research articles on their toxic, antibiotic activities, but everyone else was merchandizing phytochemicals as antioxidants, essential oils and superfoods. This is a major conceptual problem. Our bodies expend a significant fraction of our energy resources to detoxicify phytochemicals and human cultures have elaborate rituals to avoid phytochemicals and domesticate plants by breeding for the least toxic. What I missed was the implication that the pharmaceutical industry was repurposing toxic, antibiotic phytochemicals as medicines and then skipping the "antibiotic" label.

Unlabelled Antibiotic Drugs Cause the Rise of Superbugs

Overuse of antibiotics is a problem, because it damages the gut microbiome and contributes to the modern increase in autoimmunity. Food processing is another culprit and so is the mania for hyperhygiene and the demonization of bacteria. Unfortunately, the major culprit in the development of multiple antibiotic resistant superbugs is the tons of commonly used pharmaceuticals that systematically attack gut bacteria, but are not labelled as antibiotics. Most modern drugs were developed from phytochemicals and were initially used in plants to kill bacteria and fungi, i.e. phytoalexins. Pharmaceutical companies acknowledge the antibiotic activities of common drugs, by sponsoring research conferences to develop existing drugs as new classes of antibiotics for treatment of superbugs.

28 comments:

newbie
said...

Good overview, I look forward to seeing you expand on these ideas over the coming year.Clarification - have you changed your view on fermented veggies? In the past, you said dairy ferments were transient, but veggies ones were a more permanent fix. Your current post lumps both together as transient.

Also, are you suggesting that our antioxidant and supp fixation is a type of antimicrobial, pushed by big pharma (promoting them but not telling us that they are antimicrobials)? That these phytochemicals are actually hurting our good bugs?

I've been reading this blog for a couple of years now and followed the posts with great interest.

My health has much improved since ditching the medicines and concentrating on the gut flora, eating home made sauerkraut along with RS3 cooled/reheated roast potatoes practically every day. Ginger and magnesium also seem to help in my battle with chronic inflammation and calcified soft tissue.

On the subject of soil based bacteria what is the best way to obtain these? I see people buying expensive soil based probiotics but is this necessary or do we just need to get our hands dirty?

Thirty years ago when I was at school our biology teacher told us we were all too clean and that it would make us sick. He singled out one student from Nigeria and said his immune system would be much more robust than the rest of us. He even suggested that we should occasionally grab a handful of soil and drink it with a glass of water. Was this crazy talk or inspired thinking years ahead of his time? I walk in unspoilt woods every day with my dog and I'm thinking a lot of that soil must be rich bacteria but I have so far resisted the temptation to consume any.

Newbie,Dairy and fermented veggie probiotics are similar, i.e. lots of lactobacilli. In both cases the bacteria proliferate and convert available sugars to lactic acid, etc.

The complexity of the resulting "dairy" probiotics is dependent on the available contaminating bacteria. Commercial versions are much more limited, so local, homemade batches are better.

The dairy probiotics don't establish in the gut, so are temporary, but they do seem to duplicate many of the functions of a stable, complex gut flora of several hundred different species. That means to me that eating fresh, homemade fermented veggies is a good way to be sure that your immune system is working.

I suspect that slight variations in the source of veggies and preparation for fermentations, will make the probiotics in fermented veggies more varied than those in dairy, and avoid some of the antibacterial properties of milk. But note that plants are also loaded with natural antibiotics/phytoalexins/phytochemicals.

The bottom line is that a healthy gut flora adapts, so I don't sweat the natural antibiotic properties of all natural milk and veggies, as long as I continue to eat a supply of new bacteria.

I am very concerned about the intense, focused antibiotic activities of common OTC and prescription drugs.

All of the bacteria that one needs to be healthy are present in most soil and certainly in a good compost pile, but there is also an assortment of pathogens and parasites. Most people seeking to repair their gut flora by eating soil bacteria also have damaged immune systems and will be particularly vulnerable to the baddies in the soil.

Medicine has not bothered to solve this dilemma and has obvious conflicts of interest. Fecal transplants could easily be a simple remedy, but they provide another conflict of interest, because they would replace billion dollar treatments with hundred dollar cures.

In the mean time, I can only say that I personally try to get the benefits of introducing new bacteria by growing some of my own veggies, not washing raw veggies excessively, avoiding anti-bacterial soaps and avoiding medicine. I don't avoid people and kiss relatives, friends and babies. I think outdoor pets are also helpful. I also use a minimal amount of salt in homemade fermented veggies.

There is probably a good use for commercial probiotics, but most are useless and many of the included bacteria and fungi are known by the manufacturers as just available and used to pad lists. Some make sense, such as Clostridium butyricum.

I wouldn't use any probiotic capsules routinely. If they are useful for gut flora repair, then a week's use should be sufficient. Routine use of fermented veggies makes sense.

I think that your teacher was talking about the hygiene hypothesis, which was right for the wrong reasons. It is not about exposure to numerous antigens, but rather about growing a healthy gut flora that controls the development of a robust immune system.

I've been eating homemade sauerkraut now for over a year and I'm sure that has more useful bacteria than any shop bought pills plus the sauerkraut is delicious, particularly with small amounts of Himalayan salt.

More recently I've started adding goats milk yogurt or authentic Greek yoghurt to my diet, which should not be confused with Greek style yogurt. My next step will be to start making yogurt at home but I want to try and source some local unpasteurised milk. I understand these are transitory patches rather than fixes but a constant flow of good bacteria has to be better than diet of processed foods.

I really think that eating the RS3 cooked/cooled/reheated potatoes regularly has made a huge difference and helped the other elements to work more effectively. In fact I started to see an improvement after just a couple of weeks. Not long I also made some bone broth and I understand this can be beneficial in repairing the gut lining.

It's also worth mentioning that if I had eaten some potatoes or cheese for example a year ago I would have suffered extended pain for several hours from a spike in inflammation but that is now vastly improved. Having said that I still avoid all sugar, medicines and processed foods.

The way I see it I spent 40+ years inadvertently destroying my gut flora and health, so it's going to take a little while to fix. I wasn't breast fed as a baby and I've had various courses of antibiotics plus I got just about everything else wrong. Apart from fixing my own health I'm also trying to learn so that I can pass on this information to my family.

Recently I was contacted by a family friend who is desperate because her 19 year old daughter is suffering from severe Crohn's disease that the doctors are treating with immune suppressants it's making her terribly ill. I told her about these diet changes along with mentioning fecal transplants as something she could investigate. I could really sense her frustration in dealing with doctors who seem unwilling to consider anything other than their current treatments. Her daughter wasn't breast fed and suffered lots of allergies as a child that were all treated with antibiotics.

I too have been eating fermented vegetables daily for about a year and a half. I also add potato starch once a day. Take Cod Liver Oil and some other stuff. But what made a huge change in the way I actually felt was consuming fermented vegetable juice, the juice from the vegetable ferments. Store bought, but the real thing. Basically, since consuming this juice, I've gone from having lousy energy, dragging, feeling sort of weak almost all the time - for years - to having great energy, zooming along, walking fast, no problem! This is almost miraculous. Art, any thoughts? Is it possible in liquid form the bacteria are better utilized - or something?

Anony - kraut juice,First, I must speculate upon kraut juice. The juice starts with lots of easily leached material from the veggies, including sugars, salts and a few bacteria. After a few days, the bacteria have divided and consumed what they can. Most of the probiotic bacteria remain suspended in the juice. The bacteria that can live on plant polysaccharides probably start to form biofilms on the kraut.

Some of the phytochemicals in the veggies are diluted into the juice.

So juice is where most of the probiotics are plus the more hydrophilic of the phytochemicals.

Gut bacteria in biofilms and colon are probably protected from phytochemicals, whereas bacteria in the small intestines are probably more exposed.

The result of drinking kraut juice would be a dose of probiotics that stimulate normal function of the small intestines and immune system, and a dose of phytochemicals that probably help to stifle bacteria growing in the small intestines.

Zest from kraut juice is a common observation from fermentistas who notice the loss after a few days without their kraut. It is also interesting that fermentistas start just eating the kraut and inevitably move on to the juice.

I'm a gardener. When I thin lettuce, greens and onions, I eat the thinnings. I grow one cherry tomato for eating while gardening. I grow 3 different mints and a stevia plant also for eating outside. I eat about half the sugar snap peas when harvesting. I must eat gobs of bacteria.

great review,I've also just read your post on phytochemicals (and the comments).

1. Could you please tell me if I understood correctly:On the one hand - plants contain phytochemicals, on the other hand - plants contain soluble fibers.Since our liver can detoxify most phytochemicals then we should eat plants (but not go crazy with it).

2. Looking at the definition of 'hormesis' from wikipedia:"It is conjectured that low doses of toxins or other stressors might activate the repair mechanisms of the body. The repair process fixes not only the damage caused by the toxin, but also other low-level damage that might have accumulated before without triggering the repair mechanism"Do you believe that theoretically intoducing such plant phytochemicals in small amounts can cause this beneficial effect (if not - then what toxins are they talking about?)

3. Reading 'Anonymous' (20, 3:01) question and you answer makes me ask: May phytochemicals be a good help for SIBO (since they harm only the bacteria in the upper area of the digestive tract before they are digested)?

4. What do you think about 'onion' and 'garlic' - they have 8.6% and 17.5% (respectively) inulin and oligofructose according to wikipedia, yet quite strong antibacterial affect?

Art, thanks so much. This is Anonymous, the kraut juice drinker. As I said, this change in zest as you put it, is incredible, too incredible to put into words. I have been maintaining an 80 pound weight loss for about 25 years, and was obese before that - until I was 32 and lost the weight - and ate horribly even in maintenance, not to mention antibiotics prior to dental work - I was a mess. By the way, my hair loss has stopped too. But the energy thing - I never expected this. Now I am trying to determine how much of the juice I need to stay healthy and keep disease at bay.

Kraut juice drinker here again: I wonder if it's just the kraut juice and whether the other fermented juices - carrot & beet - are having the same effect? By the way, I am someone who only ate SWEET, and now an orange squash is sweet. I'll put a single stevia in a coffee and it's sweet. I used to dump in - get ready - about 10 Equal & Sweet & Low packets into a single coffee - together. Well, thankfully I have come a long way, and it took a long time, and I'm grateful.

ChenShak,1. true. Don't worry about phytochemicals in domesticated, food plants.2. no. Detox mechanisms will turn on with exposure to toxins, such as phytochemicals. That has a cost higher than the benefit of low level exposure.3. yes. Phytochemicals may help for SIBO, because phytoalexins are broad spectrum antibiotics. But they may also cause more damage. Unpredictable.4. yes. Onion and garlic are good for their prebiotic fiber, but they may cause some damage also.

In general, I don't think about phytochemicals when I eat, and am only concerned to get enough prebiotic fiber to feed my gut flora.

Hi Raj,I think that some dietary conditions may be used to increase genes needed for repair enough so that they can be transferred and then maintained. Thus, some people respond to repair their gut flora by diet alone.

Most people require new bacteria to repair damaged gut flora in addition to a diet to maintain the fixed flora.

I think that there will always be a need for a large number of separate genomes to house incompatible metabolic pathways. Thus, there will also be a need to transfer intermediates between different species. There are numerous gut niches and some change by the hour after meals/circadian.

I can't imagine any process being as cheap and easy as swallowing capsules of freeze dried feces. A treatment would cost a dollar, without a prescription.

Art, can you expound a little on the types of prebiotic fiber you make sure to consume? Do you believe in any kind of supplements for this?

A friend currently has C-Diff he contracted after antibiotic use. Now he's on more antibiotics for it, but so far no real change. I'm so concerned. I had another friend whose C-Diff seemed to finally be eradicated, and weeks later returned with a vengeance; he ended up in the hospital on an IV - which did eventually get rid of it. He continues to take a probiotic pill, which his wife for some bizarre reason mocks hm for.

Do you have any probiotic/essential oil suggestions for babies both on solids and pre solids? I work with a lot of very unhappy babies and get mostly good results using probiotics (I use Metagenics), either directly to the baby or via the mums breast milk. Unfortunately not all are able to be breast fed which leaves me with the added complication of formula. I find some become reliant on the probiotics and some are good after one to two weeks and do not require further doses. Most have been exposed to antibiotics by birth or at birth. A lot cannot tolerate any dairy exposure so I use probiotics not made off milk. Sauerkraut is out for the tiny ones. I would be interested to hear your thoughts.

Kraut juice drinker which brands do you use and how much at a time per day? I have had the leftover kraut juice before and had quite an immediate laxative effect. So, I'm wondering how low I can go and get the benefit.

S: I drink about 6 ounces of kraut - or carrot or beet - fermented juice per day. That's just an estimate. My problem is constipation, which has improved over time through diet. The juice doesn't seem to affect it much. But, as I said, my energy, or zest, seems attributable to it.

I agree that "most of the needed bacteria are more common in soil than in food". In addition to the soil based probiotics, is there a need to eat soil? And if yes, how to do it (which soil, is there any supplier to buy it online, etc)?

First "dairy probiotics don't establish in the gut"thanks Dr Ayer for this, I will not spend much money on commercial probiotics, I guess.

Also the fact that most useful bacterias are in the soil. This is fascinating. Would eating soil help? I remember I always had to wash thouroughly my hands before eating as a kid, and always had a wreck of a health with a lot of alergies. I came from a very (excessively) clean house. Could both be somewhat connected?

Would soil baceria in small amount easily survive through the stomach and small intestine?

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About Me

I grew up in San Diego and did my PhD in Molecular, Cellular and Developmental Biology (U. Colo. Boulder). I subsequently held postdoctoral research positions at the Swedish Forest Products Research Laboratories, Stockholm, U. Missouri -Colombia and Kansas State U. I was an assistant professor in the Cell and Developmental Biology Department at Harvard University, and an associate professor and Director of the Genetic Engineering Program at Cedar Crest College in Allentown, PA. I joined the faculty at the College of Idaho in 1991 and in 1997-98 I spent a six-month sabbatical at the National University of Singapore. Most recently I have focused on the role of heparin in inflammation and disease.